[Hendrik-code]

Problem

Hints naming flags that do not exist. All four survived the 2.0 flag rename:

message	flag it names	flag that exists
Subreg Mask already exists. Set -override_subreg to create it anew	-override_subreg	--override-semantic / -os
Vert Mask already exists. Set -override_vert to create it anew	-override_vert	--override-instance / -oi
Centroids already exists, will load instead. Set -override_ctd = True	-override_ctd	--override-ctd / -oc
-model_instance/-mv resolved to None	-model_instance	--model-instance / -mi

A user who follows the hint gets error: unrecognized arguments.

--input on an uncompressed NIfTI. .nii is what most converters produce, and SPINEPS cannot read
it (BIDS_FILE keys the file as nii, the pipeline asks for nii.gz). The old code appended the suffix
unconditionally:

$ spineps sample -i scan.nii -ms t2w
FileNotFoundError: -input does not exist or is not a file, got /abs/scan.nii.nii.gz

That names a path the user never typed and says nothing about compression.

Fix

• All four messages name the real flag and say what loading/overriding will do.
• --input validation, in order: append .nii.gz only if nothing exists at the path as given (so
  --input sub-01_T2w keeps working), then report a missing folder, then a missing file, then -- for a
  file that is there but is not .nii.gz -- "SPINEPS reads gzipped NIfTI images (.nii.gz), got scan.nii.
  Compress it first, e.g. 'gzip scan.nii'."
• Removes a dead if dataset == "" branch, unreachable since the path is passed through Path.absolute().
• process_dataset's logged arguments no longer include the name of the exclusion list itself.

Tests

unit_tests/test_cli_messages.py includes a guard that walks every user-facing string in entrypoint
and seg_run, extracts anything shaped like a flag, and asserts the parser accepts it -- so the next
rename cannot leave a stale hint behind. It catches all four on main, plus the .nii message.

Full suite: 229 passed, ruff clean.

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